RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis

Abstract

RNAs adopt specific structures to perform their functions, which are critical to fundamental cellular processes. For decades, these structures have been determined and modeled with strong support from computational methods. Still, the accuracy of the latter ones depends on the availability of experimental data, for example, chemical probing information that can define pseudo-energy constraints for RNA folding algorithms. At the same time, diverse computational tools have been developed to facilitate analysis and visualization of data from RNA structure probing experiments followed by capillary electrophoresis or next-generation sequencing. RNAthor, a new software tool for the fully automated normalization of SHAPE and DMS probing data resolved by capillary electrophoresis, has recently joined this collection. RNAthor automatically identifies unreliable probing data. It normalizes the reactivity information to a uniform scale and uses it in the RNA secondary structure prediction. Our web server also provides tools for fast and easy RNA probing data visualization and statistical analysis that facilitates the comparison of multiple data sets. RNAthor is freely available at http://rnathor.cs.put.poznan.pl/.

Fig 1. Workflow in the RNAthor system.

Fig 2. Scheme of the RNAthor algorithm for unreliable data exclusion.

Fig 3. Automatic and manual normalization of RNA probing data.

SHAPE (A) and DMS (C) reactivity profiles calculated by RNAthor (red) and manually (black). Correlation between RNAthor and manual analysis per nucleotide reactivity estimated for SHAPE (B) and DMS (D).

Fig 4. Example verification of the repeatability of RNA chemical probing experiments.

Comparative step plot for repeatable (A) and non-repeatable (B) replicates of Ty1 RNA probing with DMS. (C) The box-and-whisker plot and violin plot presenting the differences in reactivity data distribution obtained for repeatable and non-repeatable experiments.